Shares of Ariad Pharmaceuticals Inc. tumbled nearly 66 percent Wednesday after the Cambridge biotechnology company said it stopped enrolling patients in ongoing clinical trials of its leukemia drug because new data showed an increased number suffered blood clots and heart problems in an earlier study.

Food and Drug Administration regulators ordered a “partial clinical hold” on Ariad’s trials until the fast-growing company changes its clinical study doses and eligibility rules and the FDA updates a warning label for the drug, called Iclusig, which was approved for US sale last December and remains on the market.

It is a significant setback for one of the region’s most promising life sciences companies, and another example of the high-risk nature of the biotechnology industry, a sector where years of costly research and development can be derailed by a single negative report.

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“We made the decision, which we communicated to the FDA, that the best approach was to pause the trial enrollment while we made some amendments,” Ariad chief executive Harvey Berger said in an interview, promising to move quickly to address safety concerns.

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But investors lost no time in bailing out of Ariad’s stock, fearful that disclosure of the higher number of patients with side effects could hurt sales of Iclusig. Ariad’s shares plunged $11.31 per share to $5.83 on the Nasdaq stock exchange, the largest decline in its 19 years as a public company.

Analysts said the setback could reverse the momentum of Ariad, which last January said it would build a corporate headquarters and laboratory complex in Kendall Square. The company plans to occupy most of two five-story buildings going up on Binney Street.

“Risk profile on Ariad went significantly up and commercial prospects/visibility on the drug have gone down,” Michael J. Yee, a biotechnology analyst for RBC Capital Markets in San Francisco, wrote in a note to investors. “Overall, we think the stock will be in the penalty box and unlikely to have a material move higher since fundamentals have changed.”

Even though sales of the drug will continue, Yee cautioned that “timetables are now likely to all be pushed out” for trials aimed at expanding the number of patients eligible to receive Iclusig. Patients already taking the drug in the current clinical trials will be allowed to keep doing so.

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The once-daily pill was approved by the FDA three months ahead of schedule to treat two rare cancers — chronic myeloid leukemia and Philadelphia chromosome positive acute lymphoblastic leukemia — for patients who can’t tolerate existing therapies or have developed resistance to those medicines.

To expand that market, and win approval for Iclusig as a “front-line” treatment — one that could be prescribed by doctors for newly diagnosed leukemia patients — Ariad had been moving forward with new testing.

But as those trials progressed, the company said, follow-up data from the late-stage study that had led to Iclusig’s approval showed more patients had cardiovascular problems and blood clots known as arterial thrombosis than had previously been known. Ariad has not said how many, if any, patients have died as a result of the side effects.

Earlier documented side effects led to an FDA-required “black box” label for Iclusig, informing doctors and patients that the pill can cause blood clots and liver toxicity. Such warnings are not uncommon for drugs prescribed to severely ill cancer patients. Nonetheless, advocates for chronic myeloid leukemia patients Wednesday took note of the additional side-effects cases.

“It’s important for patients with [chronic myeloid leukemia] to stay informed about this development, and we’re monitoring it and will keep them informed as appropriate,” said Andrea Greif, a spokeswoman for the Leukemia & Lymphoma Society in White Plains, N.Y.

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Berger, Ariad’s CEO, conceded it would likely take longer now for Iclusig to win approval as a front-line treatment. But he said the company was pressing forward with changes in the clinical trial protocol, such as reducing Iclusig dosing and restricting the eligibility of patients who might be predisposed to side effects because of heart problems.

“This is an absolute priority for us to get back on track by the end of the year,” Berger said.